Unraveling grapevine taxonomic and functional soil microbiome under different edaphic conditions within a vineyard plot.

Abstract

Grapevine, mainly Vitis vinifera, occupies an elite position among crops worldwide. Soil and plant rhizosphere microbiomes are known to act as promoters of plant growth and health status. Plant root systems can select microbial communities through root exudates, while soil physicochemical parameters influence the structure and composition of the microbial community. In this work, we characterize the taxonomic composition and potential functional microbiome in combination with a large set of physicochemical parameters from the same soil samples collected at short distance (250 m) within a conventionally managed commercial vineyard plot. Metabarcoding and metagenome analysis, using amplicon and shotgun sequencing, allowed us to explore the structure and composition of the microbiomes and their functional activity. Soil microbial structure and functionality, as well as physicochemical parameters, differed between the two locations. Levels of locations elevation, boron, and sodium showed high correlation with the sample distribution of microbial community and functional genes suggesting they could affect directly the microbial community and their interaction with grapevine roots. Elevation variable, which includes a set of stochastic and deterministic factors, could have exacerbated further the differences in the microbial community and functionality. As a result, Burkholderia-Caballeronia-Paraburkholderia, Pseudomonas, Pseudoxanthomonas, and Streptomyces genera, which were described to effectively improve plant growth and resistance to abiotic stresses, were significantly more abundant in one location presenting lower levels of boron, zinc and active limestone and higher levels of sodium (within safe ranges). Microbial activity points out to have higher positive plant interactions in the same location registering genes associated with biofilm formation and quorum sensing pathways together with lipopolysaccharide biosynthesis and membrane transport. Altogether this data contributes to a better understanding of complex systems such as grapevine soil since soil physicochemical properties and microbial communities present significant variation within the vineyard, which can eventually impact wine quality.